Technical Abstract:
Amaryllidaceae tribe Hippeastreae constitute a horticulturally valuable group of approximately 180 species of American petaloid monocots, characterized by disploidy and polyploidy (x = 6, 8, 9, 10, 11; 2n = 12-150). A recent hypothesis based on ITS and chloroplast sequence data states that Hippeastreae experienced ancient diploid hybridization(s) that preceded the radiation of the major subclade, Hippeastrinae. Additionally, the Hippeastrinae have likely gone through successive events of allopolyploidization, which further obscure the inference of phylogeny and form a complex network-like pattern of evolution. We used transcriptomic data to identify putative single-copy nuclear genes in Hippeastreae and developed biotinylated RNA baits (MYbaits) to capture 48 genes longer than 2 Kb. Illumina DNA libraries were built for ~70 taxa, and pooled libraries were used in capture experiments. Captured genes were sequenced using the Illumina MiSeq platform (2x150 or 2x250 paired-end reads). Great care was taken to address the assembly of in-paralogs, which are likely to be encountered in a group with such a complex and reticulate pattern of evolution as Hippeastreae. Given the complex data, and our previous knowledge and hypotheses about the phylogeny of Hippeastreae, multiple markers were thoroughly and individually analyzed to compare gene trees. Several tests of the deep reticulation hypothesis were performed, including recombination detection, Lento plots, and network analyses. The resulting phylogenetic framework will serve as a basis for understanding patterns of character evolution in Hippeastreae and for reclassification of the tribe at the genus level.